Hello all,
I am trying to map solid 4 reads onto 5 genomes with bowtie. After inputting the contig fasta files i get the following output:
Reading reference sizes
Warning: Encountered empty reference sequence (x20)
Time reading reference sizes: 00:00:01
The script continues and gives a similar warning message later:
Total time for call to driver() for forward index: 00:00:10
Reading reference sizes
Warning: Encountered empty reference sequence (x20)
We have used the same script on other organisms without these errors. The only thing I can think of is my organisms were assembled in an automated pipeline and thus have some really small contigs. The script finishes successfully and the outputs seem to be usable. Could anyone shed some light onto what could be happening?
I am trying to map solid 4 reads onto 5 genomes with bowtie. After inputting the contig fasta files i get the following output:
Reading reference sizes
Warning: Encountered empty reference sequence (x20)
Time reading reference sizes: 00:00:01
The script continues and gives a similar warning message later:
Total time for call to driver() for forward index: 00:00:10
Reading reference sizes
Warning: Encountered empty reference sequence (x20)
We have used the same script on other organisms without these errors. The only thing I can think of is my organisms were assembled in an automated pipeline and thus have some really small contigs. The script finishes successfully and the outputs seem to be usable. Could anyone shed some light onto what could be happening?
